SHIELD operates in the MCU sort of the way NATO does in the real world. It is an organization operated as an intergovernmental alliance of a number of countries for the protection of the Earth, above any one nation's military. One would assume that individual sponsor governments have representatives on the WSC and thus have access to information on members of the Avengers.

eh, the higher you go up in military rankings the more you know... SHIELD operates ABOVE the US military.. thus, SHIELD will always know MORE. and not everyone at SHIELD has clearance to know everything either.